Although I am no expert in "bar stool protocol", my opinion is if there is a drink or food in front of the stool, then it is an occupied seat. No drink and/or food means it is an open stool.
The smoking thing is something that happens, so a short amount of time off the stool for a smoke or a toilet call is something that happens, but to hold the seat, there should be some evidence of it being used. If the bar in front of the seat is clean, the seat should be open and available to anyone.
A bartender holding a stool for a buddy or two that have not yet arrived should be fired. I would have talked to management, then walked out.
Again, I do not claim to be an expert, but I am experienced!
R2B